Traditional methods for acquiring three-dimensional (x,y,λ) hyper-spectral measurements typically require intensive computational efforts and expensive optical components. However, recent advances in fabrication techniques have allowed the creation of very precise tunable Fabry-Pérot etalons that can be used for making low-cost hyper-spectral measurements. These etalons have transmission spectrums that exhibit peaks of transmission as a function of a settable gap between two reflective glass optical flats. By collecting images using a sensor that collects light that has either passed through a Fabry-Perot etalon for a defined set of gaps, or has been reflected by a target illuminated by light passing through a Fabry-Perot etalon for a defined set of gaps, it is possible to reconstruct the full three-dimensional (x,y,λ) hyper-spectral data cube of what is being imaged by the camera. However, because the etalon typically transmits multiple narrow peaks in the spectral range of interest and the camera pixel sensitivity spectra are broad and fixed, there is not a simple one-to-one mapping of pixel measurements to source spectra for a given gap, making it difficult or impossible to directly interpret the spectral content of raw image measurements. Moreover, temperature variations within the instrument result in hyper-spectral measurement errors due to etalon gap shifts as well as light source spectral variations.